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comparison fetch_fasta_from_NCBI.xml @ 1:7e41bbb94159 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
author artbio
date Sun, 15 Oct 2017 13:56:26 -0400
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0:c877548ebde1 1:7e41bbb94159
1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="2.1.0">
2 <description></description>
3 <command><![CDATA[
4 python '$__tool_directory__'/fetch_fasta_from_NCBI.py
5 -i "$queryString"
6 -d $dbname
7 -o '$outfilename'
8 -l '$logfile'
9 #if $date_condition.date_filter == "YES":
10 --datetype $date_condition.datetype
11 --mindate $date_condition.mindate
12 --maxdate $date_condition.maxdate
13 #end if
14 ]]></command>
15
16 <inputs>
17 <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete[all] NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple:'Drosophila melanogaster[Organism] AND Gcn5[Title]">
18 <sanitizer>
19 <valid initial="string.printable">
20 <remove value="&quot;"/>
21 <remove value="\"/>
22 </valid>
23 <mapping initial="none">
24 <add source="&quot;" target="\&quot;"/>
25 <add source="\" target="\\"/>
26 </mapping>
27 </sanitizer>
28 </param>
29 <param name="dbname" type="select" label="NCBI database">
30 <option value="nuccore">Nucleotide</option>
31 <option value="protein">Protein</option>
32 </param>
33 <conditional name="date_condition">
34 <param name="date_filter" type="boolean" label="Filter the sequences by date?" truevalue="YES" falsevalue="NO" checked="false"/>
35 <when value="YES">
36 <param name="datetype" type="select">
37 <option value="pdat">Publication date</option>
38 <option value="mdat">Modification date</option>
39 </param>
40 <param name="mindate" type="text" help="Date must follow one of the following formats: YYYY/MM/DD, YYYY/MM or YYYY"/>
41 <param name="maxdate" type="text" help="Date must follow one of the following formats: YYYY/MM/DD, YYYY/MM or YYYY"/>
42 </when>
43 <when value="NO"/>
44 </conditional>
45 </inputs>
46 <outputs>
47 <data name="outfilename" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" />
48 <data format="txt" name="logfile" label="${tool.name}: log"/>
49 </outputs>
50 <tests>
51 <test>
52 <param name="queryString" value="9629650[gi]" />
53 <param name="dbname" value="nuccore" />
54 <output name="outfilename" ftype="fasta" file="output.fa" />
55 <!-- <output name="logfile" ftype="txt" file="log.txt" /> log.txt changes with timestamp. removed to pass the test -->
56 </test>
57 <test>
58 <param name="queryString" value="CU929326[Accession]" />
59 <param name="dbname" value="nuccore" />
60 <param name="date_filter" value="YES"/>
61 <param name="datetype" value="pdat"/>
62 <param name="mindate" value="2008/09"/>
63 <param name="maxdate" value="2008/09"/>
64 <output name="outfilename" ftype="fasta" file="zebra_output.fa" />
65 </test>
66 </tests>
67 <help>
68 **What it does**
69
70 This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database for a given entrez query.
71
72 The tool is preset with "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" for metaVisitor use purpose
73
74 See `Entrez help`_ for explanation of query formats
75
76 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields.
77
78 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset)
79
80 **Acknowledgments**
81
82 This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.
83
84 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
85
86 .. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
87 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon
88 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
89 .. _MIT license: http://opensource.org/licenses/MIT
90
91 </help>
92 <citations>
93 <citation type="doi">10.1186/1471-2105-14-73</citation>
94 </citations>
95 </tool>